Proovread-Teaching: Difference between revisions
No edit summary |
No edit summary |
||
| Line 40: | Line 40: | ||
<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | ||
<nowiki>#</nowiki>SBATCH --output=proovread.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=proovread.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=proovread.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
| Line 59: | Line 60: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
ml proovread/2.14.1-foss-2016b | ml proovread/2.14.1-foss-2016b | ||
NA | |||
</pre> | </pre> | ||
Revision as of 13:05, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
2.14.1
Author / Distributor
Description
"PacBio hybrid error correction through iterative short read consensus" More details are at proovread
Running Program
The last version of this application is at /usr/local/apps/eb/proovread/2.14.1-foss-2016b
To use this version, please load the module with
ml proovread/2.14.1-foss-2016b
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_proovread
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=proovread.%j.out
#SBATCH --error=proovread.%j.err
cd $SLURM_SUBMIT_DIR
ml proovread/2.14.1-foss-2016b
NA [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml proovread/2.14.1-foss-2016b NA
Installation
Source code is obtained from proovread
System
64-bit Linux